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Commit cc900bac authored by Andrey Filippov's avatar Andrey Filippov
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Before implementing tree-top filter

parent e43d01e8
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Showing with 473 additions and 418 deletions
src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java
View file @ cc900bac
......@@ -859,6 +859,7 @@ min_str_neib_fpn 0.35
// combine parameters
public boolean terr_crop = true; // Crop output image to the bounds of all segments
public int terr_border_width = 6;
public boolean terr_render_open = true; // render open areas (no vegetation offset)
public boolean terr_render_no_alpha = true; // render where no opacity is available
......@@ -876,6 +877,8 @@ min_str_neib_fpn 0.35
public double terr_min_terrain = 0.001;
public double terr_min_vegetation = 0.5;
public int terr_debug = 0;
public String terr_debug_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/lma_um/";
public int terr_debug_length = 200;
public boolean terr_debug_improved = true; // Save debug data if LMA step improved
public boolean terr_debug_worsened = true; // Save debug data if LMA step improved
......@@ -2191,6 +2194,7 @@ min_str_neib_fpn 0.35
gd.addMessage ("Combining LMA results segments");
gd.addCheckbox ("Crop result image", terr_crop, "Crop output image to the bounds of all segments.");
gd.addNumericField("Overlap width", terr_border_width, 0,3,"","Width of the inter-tile oiverlap border.");
gd.addCheckbox ("Render open", terr_render_open, "");
gd.addCheckbox ("Render no alpha", terr_render_no_alpha, "");
......@@ -2206,7 +2210,9 @@ min_str_neib_fpn 0.35
gd.addNumericField("Min max terrain", terr_min_max_terrain, 5,7,"", ".");
gd.addNumericField("Minimal terrain", terr_min_terrain, 5,7,"", ".");
gd.addNumericField("Minimal vegetation", terr_min_vegetation, 5,7,"", ".");
gd.addNumericField("LMA debug level", terr_debug, 0,3,"", ".");
gd.addNumericField("LMA debug level", terr_debug, 0,3,"", "Debug level.");
gd.addStringField ("Debug directory", terr_debug_path, 120,"Directory to save debug images.");
gd.addNumericField("Debug length", terr_debug_length, 0,3,"","Maximal number of debug image slices.");
gd.addCheckbox ("Debug improved", terr_debug_improved, "Save debug image after successful LMA step.");
gd.addCheckbox ("Debug worsened", terr_debug_worsened, "Save debug image after unsuccessful LMA step.");
......@@ -2939,6 +2945,7 @@ min_str_neib_fpn 0.35
terr_recalc_boost = gd.getNextNumber(); // double
terr_recalc_average = gd.getNextBoolean();// boolean
terr_crop = gd.getNextBoolean();// boolean
terr_border_width = (int) gd.getNextNumber(); // int
terr_render_open = gd.getNextBoolean();// boolean
terr_render_no_alpha = gd.getNextBoolean();// boolean
......@@ -2953,7 +2960,9 @@ min_str_neib_fpn 0.35
terr_min_max_terrain = gd.getNextNumber();// double
terr_min_terrain = gd.getNextNumber();// double
terr_min_vegetation = gd.getNextNumber();// double
terr_debug = (int) gd.getNextNumber(); // int
terr_debug = (int) gd.getNextNumber(); // int
terr_debug_path = gd.getNextString(); // String
terr_debug_length = (int) gd.getNextNumber(); // int
terr_debug_improved = gd.getNextBoolean();// boolean
terr_debug_worsened = gd.getNextBoolean();// boolean
// end of vegetation
......@@ -3663,6 +3672,7 @@ min_str_neib_fpn 0.35
properties.setProperty(prefix+"terr_recalc_boost", terr_recalc_boost+""); // double
properties.setProperty(prefix+"terr_recalc_average", terr_recalc_average+""); // boolean
properties.setProperty(prefix+"terr_crop", terr_crop+""); // boolean
properties.setProperty(prefix+"terr_border_width", terr_border_width+""); // int
properties.setProperty(prefix+"terr_render_open", terr_render_open+""); // boolean
properties.setProperty(prefix+"terr_render_no_alpha", terr_render_no_alpha+""); // boolean
......@@ -3677,7 +3687,9 @@ min_str_neib_fpn 0.35
properties.setProperty(prefix+"terr_min_max_terrain", terr_min_max_terrain+""); // double
properties.setProperty(prefix+"terr_min_terrain", terr_min_terrain+""); // double
properties.setProperty(prefix+"terr_min_vegetation", terr_min_vegetation+""); // double
properties.setProperty(prefix+"terr_debug", terr_debug+""); // int
properties.setProperty(prefix+"terr_debug", terr_debug+""); // int
properties.setProperty(prefix+"terr_debug_path", terr_debug_path+""); // String
properties.setProperty(prefix+"terr_debug_length", terr_debug_length+""); // int
properties.setProperty(prefix+"terr_debug_improved", terr_debug_improved+""); // boolean
properties.setProperty(prefix+"terr_debug_worsened", terr_debug_worsened+""); // boolean
// end of vegetation
......@@ -4411,6 +4423,7 @@ min_str_neib_fpn 0.35
if (properties.getProperty(prefix+"terr_recalc_boost")!= null) terr_recalc_boost=Double.parseDouble(properties.getProperty(prefix+"terr_recalc_boost"));
if (properties.getProperty(prefix+"terr_recalc_average")!= null) terr_recalc_average=Boolean.parseBoolean(properties.getProperty(prefix+"terr_recalc_average"));
if (properties.getProperty(prefix+"terr_crop")!= null) terr_crop=Boolean.parseBoolean(properties.getProperty(prefix+"terr_crop"));
if (properties.getProperty(prefix+"terr_border_width")!= null) terr_border_width=Integer.parseInt(properties.getProperty(prefix+"terr_border_width"));
if (properties.getProperty(prefix+"terr_render_open")!= null) terr_render_open=Boolean.parseBoolean(properties.getProperty(prefix+"terr_render_open"));
if (properties.getProperty(prefix+"terr_render_no_alpha")!= null) terr_render_no_alpha=Boolean.parseBoolean(properties.getProperty(prefix+"terr_render_no_alpha"));
......@@ -4426,6 +4439,8 @@ min_str_neib_fpn 0.35
if (properties.getProperty(prefix+"terr_min_terrain")!= null) terr_min_terrain=Double.parseDouble(properties.getProperty(prefix+"terr_min_terrain"));
if (properties.getProperty(prefix+"terr_min_vegetation")!= null) terr_min_vegetation=Double.parseDouble(properties.getProperty(prefix+"terr_min_vegetation"));
if (properties.getProperty(prefix+"terr_debug")!= null) terr_debug=Integer.parseInt(properties.getProperty(prefix+"terr_debug"));
if (properties.getProperty(prefix+"terr_debug_path")!= null) terr_debug_path=(String) properties.getProperty(prefix+"terr_debug_path");
if (properties.getProperty(prefix+"terr_debug_length")!= null) terr_debug_length=Integer.parseInt(properties.getProperty(prefix+"terr_debug_length"));
if (properties.getProperty(prefix+"terr_debug_improved")!= null) terr_debug_improved=Boolean.parseBoolean(properties.getProperty(prefix+"terr_debug_improved"));
if (properties.getProperty(prefix+"terr_debug_worsened")!= null) terr_debug_worsened=Boolean.parseBoolean(properties.getProperty(prefix+"terr_debug_worsened"));
// end of vegetation
......@@ -5119,6 +5134,7 @@ min_str_neib_fpn 0.35
imp.terr_recalc_boost = this.terr_recalc_boost;
imp.terr_recalc_average = this.terr_recalc_average;
imp.terr_crop = this.terr_crop;
imp.terr_border_width = this.terr_border_width;
imp.terr_render_open = this.terr_render_open;
imp.terr_render_no_alpha = this.terr_render_no_alpha;
......@@ -5134,7 +5150,8 @@ min_str_neib_fpn 0.35
imp.terr_min_terrain = this.terr_min_terrain;
imp.terr_min_vegetation = this.terr_min_vegetation;
imp.terr_debug = this.terr_debug;
imp.terr_debug_path = this.terr_debug_path;
imp.terr_debug_length = this.terr_debug_length;
imp.terr_debug_improved = this.terr_debug_improved;
imp.terr_debug_worsened = this.terr_debug_worsened;
// end of vegetation
......
src/main/java/com/elphel/imagej/vegetation/VegetationModel.java
View file @ cc900bac
......@@ -1596,14 +1596,21 @@ public class VegetationModel {
double transparency_pow = clt_parameters.imp.terr_recalc_pwr ; // 1.0; // Raise transparency to this power when calculating weight
double transparency_gb = clt_parameters.imp.terr_recalc_gb ; // 2.0; // Blur transparency-based confidence
double transparency_boost = clt_parameters.imp.terr_recalc_boost ; // 5.0; // Maximal boost while increasing low-confidence pixel weights
boolean recalc_average = clt_parameters.imp.terr_recalc_average ; //false; // apply transparency to average mismatch
boolean recalc_average = clt_parameters.imp.terr_recalc_average ; // false; // apply transparency to average mismatch
String debug_path = clt_parameters.imp.terr_debug_path; // Directory to save debug images
boolean debug_save_improved = clt_parameters.imp.terr_debug_improved;
boolean debug_save_worsened = clt_parameters.imp.terr_debug_worsened;
int debug_length = clt_parameters.imp.terr_debug_length;
// boolean restore_mode = false;
boolean save_par_files = true; // false;
String segments_dir = getSegmentsDir(segments_sub);
boolean read_pars = false; // true; /// false; /// true; // false; // true;
boolean crop_combo = clt_parameters.imp.terr_crop; // Crop output image to the bounds of all segments
// debug feature to read to continue - needs to be cleaned up/replaced
// String parameters_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/essential/parameters_vector_data_x143-y317-w35-h35-al100.0-alo0.0-alp10.0-alin-tl0.2-vl0.01-tp0.01-vp0.01-bp5.0-um1.0_0.8.tiff";
......@@ -2061,7 +2068,6 @@ public class VegetationModel {
segments_dir, // String dir_path)
segments_suffix); // String suffix);
*/
boolean crop_combo = true;
VegetationSegment [] segments = vegetationLMA.readAllSegments(
segments_dir, // String dir_path)
segments_suffix, // String suffix);
......@@ -2072,6 +2078,7 @@ public class VegetationModel {
transparency_pow, // double transparency_pow,
transparency_gb, // double transparency_gb,
debugLevel, // int debugLevel,
debug_path, // String debug_path,
debug_save_improved, // boolean debug_save_improved, // Save debug image after successful LMA step.");
debug_save_worsened); // boolean debug_save_worsened) { // Save debug image after unsuccessful LMA step.");
VegetationSegment.combineSegments(
......@@ -2116,9 +2123,11 @@ public class VegetationModel {
int num_samples = vegetationLMA.prepareLMA(
false, // final boolean keep_parameters,
woi, // final Rectangle woi,
null, // final Rectangle woi_veg_in, // used when loading from file (may be different)
max_warp, // final double max_warp, // 1.8 - do not use scenes where distance between vegetation projection exceeds this
max_offset, // final int max_offset, // maximal "elevation" to consider
elevation_radius, // final double elevation_radius, // Radius of elevation/vegetation influence.
null, // final boolean [] valid_scene_pix,
hifreq_weight, //final double hifreq_weight, // 22.5 0 - do not use high-freq. Relative weight of laplacian components
terrain_correction,// final double terrain_correction,
fit_terr, // final boolean adjust_terr,
......@@ -2158,8 +2167,9 @@ public class VegetationModel {
max_parallax, //final double max_parallax, // do not consider maximal parallax above this (consider it a glitch)
// um_sigma, // final double um_sigma, // just use in debug image names
// (um_en? um_weight: 0.0), // final double um_weight,
// par_path, // final String parameters_read_path,
debugLevel, // final int debugLevel);
// par_path, // final String parameters_read_path,
debugLevel, // final int debugLevel);
debug_path, // final String debug_path,
debug_save_improved, // final boolean debug_save_improved, // Save debug image after successful LMA step.");
debug_save_worsened);// final boolean debug_save_worsened) // Save debug image after unsuccessful LMA step.");
......@@ -2168,17 +2178,38 @@ public class VegetationModel {
continue;
}
// if (save_par_files && skip_existing_woi) { // check that segment already exists
if (save_par_files && skip_existing_woi) { // check that segment already exists
// public boolean segmentFileExist(String dir_path) {
/*
String save_path = VegetationLMA.getSavePath(
segments_dir, // String dir,
vegetationLMA.getParametersDebugTitle()); // String title)
if (new File (save_path).exists()) {
System.out.println("File "+save_path+"\n already exists, skipping this woi");
continue;
}
if (new File (save_path.replace("-new-","-file-")).exists()) {
System.out.println("File "+save_path+"\n already exists, skipping this woi");
continue;
*/
File[] segment_files = vegetationLMA.getSegmentFiles(segments_dir);
if (tile_woi) {
if (segment_files.length > 0) {
for (File f : segment_files) {
System.out.println("File "+f+"\n with the same woi already exists, skipping this woi");
}
continue;
}
} else {
String save_path = VegetationLMA.getSavePath(
segments_dir, // String dir,
vegetationLMA.getParametersDebugTitle()); // String title)
if (new File (save_path).exists()) {
System.out.println("File "+save_path+"\n (exactly) already exists, skipping this woi");
// for (File f : segment_files) {
// System.out.println("File "+f+"\n (exactly) already exists, skipping this woi");
// }
continue;
}
if (new File (save_path.replace("-new-","-file-")).exists()) {
System.out.println("File "+save_path+"\n already exists, skipping this woi");
continue;
}
}
}
int num_iter = num_iters[step_restore]; //
......@@ -2250,7 +2281,8 @@ public class VegetationModel {
}
/// next_run = true;
vegetationLMA.debug_index = 0;
vegetationLMA.debug_image = new double [100][]; // num_iter][];
vegetationLMA.debug_length = debug_length;
vegetationLMA.debug_image = new double [vegetationLMA.debug_length][]; // num_iter][];
int lma_rslt= vegetationLMA.runLma( // <0 - failed, >=0 iteration number (1 - immediately)
lambda, // double lambda, // 0.1
......
src/main/java/com/elphel/imagej/vegetation/VegetationSegment.java
View file @ cc900bac
......@@ -15,6 +15,7 @@ public class VegetationSegment {
public double [][] tva; // woi_veg
public double terrain_offset;
public double [] confidence; // woi
public boolean [] overlaid;
public String path;
public VegetationSegment(
String path,
......@@ -23,7 +24,8 @@ public class VegetationSegment {
double terrain_offset,
double [] scene_offsets, // has NaNs
double [][] tva,
double [] confidence) {
double [] confidence,
boolean [] overlaid) {
this.path = path;
this.woi = woi;
this.woi_veg = woi_veg;
......@@ -31,6 +33,22 @@ public class VegetationSegment {
this.tva = tva;
this.terrain_offset = terrain_offset;
this.confidence = confidence;
this.overlaid = overlaid;
correctTerrainOffset();
}
public void correctTerrainOffset() {
if (!Double.isNaN(terrain_offset) && (overlaid != null)) {
int woi_length = woi.width * woi.height;
for (int windx = 0; windx < woi_length; windx++) {
int wx = windx % woi.width;
int wy = windx / woi.height;
int wvindx = (wx + woi.x - woi_veg.x) + (wy + woi.y - woi_veg.y) * woi_veg.width;
if (overlaid[windx]) {
tva[0][wvindx] += terrain_offset;
}
}
}
}
public static Rectangle getBounds( // [0] - woi, [1] - woi_weg
......@@ -98,7 +116,7 @@ public class VegetationSegment {
int x = wx + woi.x - out_woi.x;
int y = wy + woi.y - out_woi.y;
int indx = x + y * out_woi.width;
preview_data[t][ns][indx] = woi_tva[t][wsrc];
preview_data[t][ns][indx] = woi_tva[t][wsrc]; // java.lang.ArrayIndexOutOfBoundsException: Index -43 out of bounds for length 550
}
break;
case 1: // vegetation
......@@ -156,13 +174,14 @@ public class VegetationSegment {
}
VegetationModel vegetationModel = vegetationLMA.getModel();
String ref_scene = vegetationModel.reference_scene;
String pre_title = ref_scene+"-preview_segments-"+out_woi.x+"-"+out_woi.y+"-"+out_woi.width+"-"+out_woi.height;
ShowDoubleFloatArrays.showArraysHyperstack(
preview_data, // double[][][] pixels,
out_woi.width, // int width,
ref_scene+"-preview_segments", // String title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,
titles, // String [] titles, // all slices*frames titles or just slice titles or null
top_titles, // String [] frame_titles, // frame titles or null
true); // boolean show)
preview_data, // double[][][] pixels,
out_woi.width, // int width,
pre_title, // String title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,
titles, // String [] titles, // all slices*frames titles or just slice titles or null
top_titles, // String [] frame_titles, // frame titles or null
true); // boolean show)
double [] terrain_reference = crop(
vegetationModel.terrain_scenes_render[vegetationModel.reference_index],
......@@ -185,13 +204,23 @@ public class VegetationSegment {
um_weight); // final double um_weight)
String [] result_titles = {"ref_render", "terrain_accum",String.format("terrain_accum_UM%5.2f-%4.2f",um_sigma,um_weight),"terrain"};
double [][] result_img = {terrain_reference,terrain_accumulated,terrain_um,preview_data[0][accum_indx]};
// ref_scene+"-result-terrain"
boolean normalize = true;
int norm_index = 1;
if (normalize) {
result_img = normalize (
result_img, // final double [][] data,
norm_index); // final int norm_index){
}
String res_title = ref_scene+"-result_terrain-"+out_woi.x+"-"+out_woi.y+"-"+out_woi.width+"-"+out_woi.height;
if (normalize) {
res_title+= "-normalized"+norm_index;
}
ShowDoubleFloatArrays.showArrays(
result_img,
out_woi.width,
out_woi.height,
true,
ref_scene+"-result_terrain",
res_title,
result_titles);
......@@ -439,6 +468,68 @@ public class VegetationSegment {
}
return cropped;
}
/**
* Normalize slices to match the selected one by average and standard deviation
* @param data array of image slices
* @param norm_index index (0-based) of the reference slice
* @return normalized image
*/
public static double [][] normalize (
final double [][] data,
final int norm_index){
final int num_slices = data.length;
final int num_pix = data[0].length;
double [][] normalized = new double [num_slices][];
for (int i = 0; i < num_slices; i++) {
normalized[i] = data[i].clone();
}
final double [] mean = new double[num_slices];
final double [] std = new double[num_slices];
final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) { // first sum for pairs
threads[ithread] = new Thread() {
public void run() {
for (int nSlice = ai.getAndIncrement(); nSlice < num_slices; nSlice = ai.getAndIncrement()) {
double [] slice = normalized[nSlice];
double s0=0, s1=0, s2=0;
for (int i = 0; i < slice.length; i++) if (!Double.isNaN(slice[i])) {
s0 += 1;
s1 += slice[i];
s2 += slice[i]*slice[i];
}
s1 /= s0;
s2 /= s0;
mean[nSlice] = s1;
std[nSlice] = Math.sqrt(s2 - s1 * s1);
}
}
};
}
ImageDtt.startAndJoin(threads);
final double [] a = new double [num_slices], b = new double[num_slices];
Arrays.fill(a, 1);
for (int n = 0; n < num_slices; n++) if (n != norm_index){
a[n] = std[norm_index]/std[n];
b[n] = mean[norm_index] - a[n]*mean[n];
}
ai.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) { // first sum for pairs
threads[ithread] = new Thread() {
public void run() {
for (int nPix = ai.getAndIncrement(); nPix < num_pix; nPix = ai.getAndIncrement()) {
for (int n = 0; n < num_slices; n++) if (n != norm_index){
double d = normalized[n][nPix];
if (!Double.isNaN(d)) {
normalized[n][nPix] = a[n]*d + b[n];
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return normalized;
}
}
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